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update field div output cols
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adelegem committed Nov 20, 2024
1 parent 5b8486a commit 8487ce0
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15 changes: 10 additions & 5 deletions R/calculate_field_diversity.R
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ calculate_field_diversity <- function(survey_data){

# loop thru each unique site
for (survey in ausplot_surveys) {
# Filter data for the current site
# filter data for the current site
site_survey_data <- survey_data |>
dplyr::filter(site_unique == survey)

Expand All @@ -48,19 +48,24 @@ calculate_field_diversity <- function(survey_data){
inv_simpson <- vegan::diversity(community_matrix[, -1], index = 'invsimpson')

subplot_diversity <- subplot_diversity |>
dplyr::mutate(shannon_diversity = shannon_diversity,
dplyr::mutate(site_location_name = substr(survey, 1, 10),
shannon_diversity = shannon_diversity,
simpson_diversity = simpson_diversity,
pielou_evenness = shannon_diversity / log(species_richness),
exp_shannon = exp(shannon_diversity),
inv_simpson = inv_simpson,
survey = survey)
inv_simpson = inv_simpson)

# order columns
subplot_diversity <- subplot_diversity |>
dplyr::select(site_location_name, everything())


# store result for current site
all_site_results[[survey]] <- subplot_diversity
}

# combine into one df
field_diversity <- dplyr::bind_rows(all_site_results, .id = "site")
field_diversity <- dplyr::bind_rows(all_site_results, .id = "site_unique")

return(list(
field_diversity = field_diversity,
Expand Down
30 changes: 15 additions & 15 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -34,25 +34,16 @@ library(saltbush)
remotes::install_github("traitecoevo/saltbush")
```

## Usage

## Spectral metrics

### Spectral diversity metrics:

+ co-efficient of variance (CV)
+ spectral variance (SV)
+ convex hull volume (CHV)

### Taxonomic diversity metrics:

+ species richness
+ shannon's diversity index
+ simpson's diversity index
+ pielou's evenness
+ exponential shannon's index
+ inverse simpson's index

## Usage

## Spectral metrics

1. List raster files and area of interest files

```{r}
Expand Down Expand Up @@ -84,15 +75,24 @@ head(metrics)

## Taxonomic metrics

### Taxonomic diversity metrics:

+ species richness
+ shannon's diversity index
+ simpson's diversity index
+ pielou's evenness
+ exponential shannon's index
+ inverse simpson's index

1. Download example plot data from AusPlots. The `veg.PI` part extracts the point intercept data from the AusPlots data structure.

```{r}
my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NTASTU0002"), veg.PI=TRUE)$veg.PI
```

2. Calculate diversity from the point intercepts using different diversity metrics
2. Calculate diversity from the point intercepts using different diversity metrics. The output is a list which includes taxonomic metrics, and also community matrices for checks.

```{r}
field_diversity <- calculate_field_diversity(my.data)
field_diversity
field_diversity$field_diversity
```
107 changes: 26 additions & 81 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -21,25 +21,16 @@ calculate spectral + taxonomic diversity values for assessment of the
remotes::install_github("traitecoevo/saltbush")
```

## Usage

## Spectral metrics

### Spectral diversity metrics:

- co-efficient of variance (CV)
- spectral variance (SV)
- convex hull volume (CHV)

### Taxonomic diversity metrics:

- species richness
- shannon’s diversity index
- simpson’s diversity index
- pielou’s evenness
- exponential shannon’s index
- inverse simpson’s index

## Usage

## Spectral metrics

1. List raster files and area of interest files

``` r
Expand Down Expand Up @@ -79,6 +70,15 @@ head(metrics)

## Taxonomic metrics

### Taxonomic diversity metrics:

- species richness
- shannon’s diversity index
- simpson’s diversity index
- pielou’s evenness
- exponential shannon’s index
- inverse simpson’s index

1. Download example plot data from AusPlots. The `veg.PI` part extracts
the point intercept data from the AusPlots data structure.

Expand All @@ -97,75 +97,20 @@ my.data <- ausplotsR::get_ausplots(my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NT
```

2. Calculate diversity from the point intercepts using different
diversity metrics
diversity metrics. The output is a list which includes taxonomic
metrics, and also community matrices for checks.

``` r
field_diversity <- calculate_field_diversity(my.data)
field_diversity
#> $field_diversity
#> site species_richness shannon_diversity simpson_diversity pielou_evenness exp_shannon
#> 1 SATFLB0004-58658 28 2.379688 0.8649789 0.7141483 10.801533
#> 2 NTASTU0002-58429 22 2.200076 0.8509874 0.7117585 9.025696
#> 3 QDAMGD0022-53501 20 2.179534 0.8242833 0.7275464 8.842187
#> 4 SATFLB0004-53705 18 2.149992 0.8375000 0.7438460 8.584786
#> inv_simpson survey
#> 1 7.406252 SATFLB0004-58658
#> 2 6.710843 NTASTU0002-58429
#> 3 5.690977 QDAMGD0022-53501
#> 4 6.153846 SATFLB0004-53705
#>
#> $community_matrices
#> $community_matrices$`SATFLB0004-58658`
#> Acacia pravifolia Alectryon oleifolius subsp. canescens Arthropodium
#> 1 2 1 13
#> Bursaria spinosa subsp. spinosa Callitris glaucophylla Carrichtera annua Cassinia laevis
#> 1 12 110 23 17
#> Daucus glochidiatus Dodonaea viscosa subsp. angustissima Eremophila deserti Eucalyptus intertexta
#> 1 1 37 1 115
#> Hakea leucoptera subsp. leucoptera Leiocarpa semicalva subsp. semicalva
#> 1 42 1
#> Lomandra multiflora subsp. dura Millotia Na Olearia decurrens Oxalis perennans
#> 1 1 3 7 18 1
#> Pauridia glabella var. glabella Poaceae Ptilotus obovatus Rhagodia parabolica Scleranthus pungens
#> 1 8 2 22 49 3
#> Sida petrophila Triodia Wahlenbergia Wurmbea Xanthorrhoea quadrangulata
#> 1 2 1 1 1 2
#>
#> $community_matrices$`NTASTU0002-58429`
#> Atalaya hemiglauca Bauhinia cunninghamii Brachychiton diversifolius subsp. diversifolius
#> 1 1 2 3
#> Brachychiton paradoxus Chrysopogon fallax Corymbia confertiflora Corymbia polycarpa
#> 1 1 77 21 47
#> Corymbia terminalis Dichanthium fecundum Dodonaea oxyptera Dolichandrone filiformis
#> 1 103 98 2 2
#> Erythrophleum chlorostachys Eucalyptus chlorophylla Eucalyptus pruinosa Eulalia aurea
#> 1 25 29 26 6
#> Flueggea virosa subsp. melanthesoides Gardenia ewartii subsp. ewartii Glycine tomentella Na
#> 1 1 3 6 2
#> Schizachyrium fragile Terminalia canescens Themeda triandra
#> 1 1 8 168
#>
#> $community_matrices$`QDAMGD0022-53501`
#> Amaranthus mitchellii Aristida latifolia Astrebla elymoides Astrebla pectinata
#> 1 1 7 27 57
#> Boerhavia schomburgkiana Bothriochloa ewartiana Cenchrus ciliaris Chloris pectinata
#> 1 1 6 32 1
#> Cynodon convergens Cyperus gilesii Dactyloctenium radulans Eulalia aurea Iseilema vaginiflorum Na
#> 1 1 3 4 3 2 2
#> Neptunia dimorphantha Poaceae Sida fibulifera Sida goniocarpa Sporobolus actinocladus
#> 1 1 11 4 4 5
#> Vachellia farnesiana
#> 1 3
#>
#> $community_matrices$`SATFLB0004-53705`
#> Acacia ligulata Alectryon oleifolius Bursaria spinosa subsp. spinosa Callitris glaucophylla
#> 1 1 7 4 108
#> Carrichtera annua Cassinia laevis Dodonaea viscosa subsp. angustissima Eremophila deserti
#> 1 5 19 16 7
#> Eucalyptus intertexta Hakea leucoptera Olearia decurrens Ptilotus obovatus Rhagodia parabolica
#> 1 97 32 10 31 43
#> Scleranthus pungens Senna artemisioides subsp. x artemisioides Sida petrophila Triodia
#> 1 1 1 15 1
#> Xanthorrhoea quadrangulata
#> 1 3
field_diversity$field_diversity
#> site_unique site_location_name species_richness shannon_diversity simpson_diversity
#> 1 SATFLB0004-58658 SATFLB0004 28 2.379688 0.8649789
#> 2 NTASTU0002-58429 NTASTU0002 22 2.200076 0.8509874
#> 3 QDAMGD0022-53501 QDAMGD0022 20 2.179534 0.8242833
#> 4 SATFLB0004-53705 SATFLB0004 18 2.149992 0.8375000
#> pielou_evenness exp_shannon inv_simpson
#> 1 0.7141483 10.801533 7.406252
#> 2 0.7117585 9.025696 6.710843
#> 3 0.7275464 8.842187 5.690977
#> 4 0.7438460 8.584786 6.153846
```

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